Grammatical Immune System Evolution for Reverse Engineering Nonlinear Dynamic Bayesian Models

An artificial immune system algorithm is introduced in which nonlinear dynamic models are evolved to fit time series of interacting biomolecules. This grammar-based machine learning method learns the structure and parameters of the underlying dynamic model. In silico immunogenetic mechanisms for the generation of model-structure diversity are implemented with the aid of a grammar, which also enforces semantic constraints of the evolved models. The grammar acts as a DNA repair polymerase that can identify recombination and hypermutation signals in the antibody (model) genome. These signals contain information interpretable by the grammar to maintain model context. Grammatical Immune System Evolution (GISE) is applied to a nonlinear system identification problem in which a generalized (nonlinear) dynamic Bayesian model is evolved to fit biologically motivated artificial time-series data. From experimental data, we use GISE to infer an improved kinetic model for the oxidative metabolism of 17β-estradiol (E2), the parent hormone of the estrogen metabolism pathway

N identical particles under quantum confinement: A many-body dimensional perturbation theory approach

Systems that involve N identical interacting particles under quantum confinement appear throughout many areas of physics, including chemical, condensed matter, and atomic physics. In this paper, we present the methods of dimensional perturbation theory, a powerful set of tools that uses symmetry to yield simple results for studying such many-body systems. We present a detailed discussion of the dimensional continuation of the N-particle Schrodinger equation, the spatial dimension D -> infinity equilibrium (D^0) structure, and the normal-mode (D^{-1}) structure. We use the FG matrix method to derive general, analytical expressions for the many-body normal-mode vibrational frequencies, and we give specific analytical results for three confined N-body quantum systems: the N-electron atom, N-electron quantum dot, and N-atom inhomogeneous Bose-Einstein condensate with a repulsive hardcore potential

The SEA-change model in information literacy: assessing information literacy development with reflective writing

Reflective writing is a key professional skill, and the University of Sheffield Information School seeks to develop this skill in our students through the use of reflective assessments. Reflection has been used as a means of supporting Information Literacy development in the Higher Education context and recent pedagogical IL frameworks highlight the important role of reflection. This paper presents an analysis of Undergraduate students’ reflective writing on one module. The writing is mapped against two models of reflection to understand the nature and depth of the students’ reflection and through this understand their Information literacy development, with the overall aim of improving the teaching and learning experience for the future. Key findings are that students did reflect deeply and identified a number of ways in which they felt their IL had developed (e.g. developing a knowledge of specialist sources), ways they could have improved their information literacy practices (e.g. through storing information in a more organised fashion), and ways that we could improve our teaching (e.g. by providing appropriate scaffolding for the activities)

Highly anisotropic Bose-Einstein condensates: crossover to lower dimensionality

We develop a simple analytical model based on a variational method to explain the properties of trapped cylindrically symmetric Bose-Einstein condensates (BEC) of varying degrees of anisotropy well into regimes of effective one dimension (1D) and effective two dimension (2D). Our results are accurate in regimes where the Thomas-Fermi approximation breaks down and they are shown to be in agreement with recent experimental data.Comment: 4 pages, 2 figures; significantly more new material added; title and author-list changed due to changes in conten

APOBEC Mutagenesis Inhibits Breast Cancer Growth through Induction of T cell-Mediated Antitumor Immune Responses

The APOBEC family of cytidine deaminases is one of the most common endogenous sources of mutations in human cancer. Genomic studies of tumors have found that APOBEC mutational signatures are enriched in theHER2 subtype of breast cancer and are associated with immunotherapy response in diverse cancer types. However, the direct consequences of APOBEC mutagenesis on the tumor immune microenvironment have not been thoroughly investigated. To address this, we developed syngeneic murine mammary tumor models with inducible expression of APOBEC3B. We found that APOBEC activity induced antitumor adaptive immune responses and CD4 T cell-mediated, antigen-specific tumor growth inhibition. Although polyclonal APOBEC tumors had a moderate growth defect, clonal APOBEC tumors were almost completely rejected, suggesting that APOBEC-mediated genetic heterogeneity limits antitumor adaptive immune responses. Consistent with the observed immune infiltration in APOBEC tumors, APOBEC activity sensitized HER2-driven breast tumors to anti- CTLA-4 checkpoint inhibition and led to a complete response to combination anti-CTLA-4 and anti-HER2 therapy. In human breast cancers, the relationship between APOBEC mutagenesis and immunogenicity varied by breast cancer subtype and the frequency of subclonal mutations. This work provides a mechanistic basis for the sensitivity of APOBEC tumors to checkpoint inhibitors and suggests a rationale for using APOBEC mutational signatures and clonality as biomarkers predicting immunotherapy response in HER2-positive (HER2 ) breast cancers

Reflection for learning: understanding the value of reflective writing for information literacy development

Reflective writing has long been acknowledged as an important aspect of personal and professional development. There is increasing evidence of the use of reflective writing assessments and activities in the context of information literacy education, particular in Higher Education. Writing reflectively can help students to understand their own information literacy development and engage in deeper learning. Students on an undergraduate Business Intelligence module at the University of Sheffield iSchool completed a piece of reflective writing about their information literacy development as part of the assessed work for the module. This writing was mapped against a model of reflection and a model of information literacy to understand the depth and spread of reflection offered by these students. The results showed that students had chosen to reflect in some but not all areas of Information Literacy, and the depth of reflection was variable. However the aspects of information literacy where students were reflective illustrated that the learning outcomes of the module had been met. Mapping reflective statements against models of reflection was found to aid in the analysis and assessment of the reflective writing. The analysis undertaken by the researchers supported their own reflective practice as Scholars of Teaching and Learning

Freshwater and anadromous fishing in Ice Age Beringia

While freshwater and anadromous fish have been critical economic resources for late prehistoric and modern Native Americans, the origin and development of fishing is not well understood. We document the earliest known human use of freshwater and anadromous fish in North America by 13,000 and 11,800 years ago, respectively, from primary anthropogenic contexts in central Alaska (eastern Beringia). Fish use appears conditioned by broad climatic factors, as all occurrences but one are within the Younger Dryas chronozone. Earlier Bølling- Allerød and later early Holocene components, while exhibiting similar organic preservation, did not yield evidence of fishing, suggesting that this was a response to changing environmental factors, perhaps reductions in higher ranked resources such as large terrestrial mammals. Late Pleistocene and recent Indigenous peoples harvested similar fish taxa in the region (salmon, burbot, whitefish, and pike). We characterize late Pleistocene fishing in interior Beringia as an important element of broad-spectrum foraging rather than the intensive communal fishing and storage common among recent peoples. © 2023 The Authors.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]